How do canonical tags work when you have multiple versions of a website?

Question

I apologize for how vague the question sounds; I was not able to write the complete question in the title because I ran out of characters. Before the duplicate monsters close the question, please read the entire question.

THE SCENARIO:

1. I have a mobile and desktop version of a website.
2. The mobile pages have canonical links pointing to the corresponding desktop version of the page.
3. The canonical links on the mobile pages are automatically generated and cannot be altered.
4. The canonical links on the desktop pages are not automatically generated but they can be added and altered.

THE SETUP:

If I have this page: http://www.example.com/phone/great-page.html

and it has a canonical link of:

<link rel="canonical" href="http://www.example.com/great-page.html">

but I want to have http://www.example.com/phone/great-page.html canonical link to:

<link rel="canonical" href="http://www.example.com/even-greater-page.html">

THE QUESTION:

Will a search engine...

a. crawl the mobile page, look to the desktop page, find a different canonical link than the page it came from, and ignore both of the canonical tags?

b. crawl the mobile page, look to the desktop page, find a different canonical link than the page it came from, and honor both canonical tags?

I know that whether a search engine honors the canonical also depends on the reliability of the previously crawled canonical tags. So for the sake of this post, let's assume that the website's previous canonical tags have been deemed reliable by the search engine.

Answer 1

This is not a good setup. Canonical pointing to page with different canonical will surely lead to problems (including indexation and rankings), sooner or later. The best scenario in your particular example is to 301 redirect the http://www.example.com/phone/great-page.html to http://www.example.com/phone/even-greater-page.html.

The best practice is to use the rel=canonical in the mobile version to the desktop , and rel=alternate in the desktop version to the mobile.